Align UPF0237 protein MMP0657 (characterized, see rationale)
to candidate WP_012965116.1 FERP_RS02985 phosphoserine phosphatase SerB
Query= uniprot:Q6LZH1 (90 letters) >NCBI__GCF_000025505.1:WP_012965116.1 Length = 391 Score = 71.6 bits (174), Expect = 7e-18 Identities = 33/78 (42%), Positives = 53/78 (67%) Query: 1 MENVVITVVGVDKPGIVAEVTKVLAQNSANIVDIRQTIMEDLFTMIMLVDISKISSDFSE 60 M+ + ++V G DKPGIV +++VLA+N+ NIVDI QT+++ +F M ++ D+ K E Sbjct: 1 MKLIAVSVYGEDKPGIVYGISEVLAENNVNIVDIEQTVLQGMFLMFIVGDVEKCKISLEE 60 Query: 61 LNVALEKLGSEIGVKINV 78 L L++ G EIGV ++V Sbjct: 61 LERKLKEKGEEIGVDVHV 78 Score = 43.1 bits (100), Expect = 3e-09 Identities = 26/85 (30%), Positives = 47/85 (55%), Gaps = 2/85 (2%) Query: 6 ITVVGVDKPGIVAEVTKVLAQNSANIVDIRQTIMEDLFTMIMLVDISKISSDFSELNVAL 65 IT++G D+ GIV +VTK+L Q+ NI T + L ++ +VD+ + +D ++ L Sbjct: 94 ITIIGRDRVGIVRDVTKILYQHGINIEKTSLTARDQLISITFVVDVRE--ADPEKVKKQL 151 Query: 66 EKLGSEIGVKINVQHENIFKYMHRI 90 ++ + G+ I +Q I K R+ Sbjct: 152 KEEIEKTGLDIVIQPYEIAKKQKRL 176 Lambda K H 0.320 0.136 0.355 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 96 Number of extensions: 4 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 90 Length of database: 391 Length adjustment: 19 Effective length of query: 71 Effective length of database: 372 Effective search space: 26412 Effective search space used: 26412 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 44 (21.6 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory